1TSU
CRYSTAL STRUCTURE OF DECAMER NCP1 SUBSTRATE PEPTIDE IN COMPLEX WITH WILD-TYPE D25N HIV-1 PROTEASE VARIANT
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MTR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 298 | SODIUM PHOSPHATE, SODIUM CITRATE, AMMONIUM SULPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.058 | α = 90 |
b = 57.731 | β = 90 |
c = 61.495 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 220 | IMAGE PLATE | RIGAKU RAXIS | OSMIC MIRRORS | 2002-10-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.1 | 42.26 | 94.1 | 0.092 | 10450 | 10450 | -3 | -3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1MTR | 2.1 | 42.26 | -3 | 9912 | 9912 | 493 | 93.93 | 0.20717 | 0.20587 | 0.23355 | RANDOM | 40.067 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1 | -0.34 | 1.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 9.961 |
r_scbond_it | 7.225 |
r_mcangle_it | 5.128 |
r_dihedral_angle_1_deg | 4.286 |
r_mcbond_it | 3.623 |
r_angle_refined_deg | 1.462 |
r_xyhbond_nbd_refined | 0.52 |
r_symmetry_vdw_refined | 0.465 |
r_symmetry_hbond_refined | 0.31 |
r_nbd_refined | 0.248 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1526 |
Nucleic Acid Atoms | |
Solvent Atoms | 112 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
AMoRE | phasing |